7-50479485-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000444124.7(DDC):​c.1021+302C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 151,712 control chromosomes in the GnomAD database, including 22,498 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.54 ( 22498 hom., cov: 33)

Consequence

DDC
ENST00000444124.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.345
Variant links:
Genes affected
DDC (HGNC:2719): (dopa decarboxylase) The encoded protein catalyzes the decarboxylation of L-3,4-dihydroxyphenylalanine (DOPA) to dopamine, L-5-hydroxytryptophan to serotonin and L-tryptophan to tryptamine. Defects in this gene are the cause of aromatic L-amino-acid decarboxylase deficiency (AADCD). AADCD deficiency is an inborn error in neurotransmitter metabolism that leads to combined serotonin and catecholamine deficiency. Multiple alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jun 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DDCNM_001082971.2 linkuse as main transcriptc.1021+302C>T intron_variant ENST00000444124.7 NP_001076440.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DDCENST00000444124.7 linkuse as main transcriptc.1021+302C>T intron_variant 1 NM_001082971.2 ENSP00000403644 P1P20711-1

Frequencies

GnomAD3 genomes
AF:
0.542
AC:
82195
AN:
151596
Hom.:
22460
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.493
Gnomad AMI
AF:
0.436
Gnomad AMR
AF:
0.617
Gnomad ASJ
AF:
0.612
Gnomad EAS
AF:
0.440
Gnomad SAS
AF:
0.513
Gnomad FIN
AF:
0.479
Gnomad MID
AF:
0.509
Gnomad NFE
AF:
0.572
Gnomad OTH
AF:
0.567
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.542
AC:
82294
AN:
151712
Hom.:
22498
Cov.:
33
AF XY:
0.538
AC XY:
39898
AN XY:
74178
show subpopulations
Gnomad4 AFR
AF:
0.493
Gnomad4 AMR
AF:
0.617
Gnomad4 ASJ
AF:
0.612
Gnomad4 EAS
AF:
0.441
Gnomad4 SAS
AF:
0.513
Gnomad4 FIN
AF:
0.479
Gnomad4 NFE
AF:
0.572
Gnomad4 OTH
AF:
0.566
Alfa
AF:
0.545
Hom.:
2796
Bravo
AF:
0.549
Asia WGS
AF:
0.526
AC:
1830
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.22
DANN
Benign
0.41

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11575461; hg19: chr7-50547183; API